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I prefer internal rad mounts (mostly for the aesthetics) and there is very little penalty for doing so.
The hot (relatively speaking) exhaust air from a rad is only a degree or two higher than room ambient and the airflow can help in a case without a heatsink/fan.
I would suspect that fan noise would be similar between an external or internal mount, so that's a non-issue.
I think the biggest determining factor would be case size.
Unless you are extremely clever and handy, an internal setup will typically require a larger case to easily fit a waterloop, although examples abound of small(ish) cases with ingenious internal solutions.